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Gut Analysis Toolbox

Name

Gut Analysis Toolbox

Software

Fiji

Author

Pradeep Rajasekhar

Maintainer

Pradeep Rajasekhar

Source

on GitHub


Gut Analysis Toolbox enables semi-automated analysis of the neuronal and glial distribution within the gut wall (enteric nervous system). It uses a combination of FIJI macros, StarDist, CLIJ and deepImageJ for segmentation and analysis.

/media/plugins/Gut_Analysis_Toolbox/summary_figure.png

Click here to access the WIKI detailed instructions on how to use GAT.A detailed how to use instructions with wiki is available here:

You can also watch tutorials for GAT on Youtube.

What you can do with GAT:

  • Semi-automated analysis of number of enteric neurons: Uses pan-neuronal marker Hu or anything with similar labelling
  • Normalise counts to the number of ganglia.
  • Count number of neuronal subtypes, such as ChAT, nNOS etc..
  • Spatial analysis using number of neighboring cells.
  • Calcium imaging analysis: Alignment of images and extraction of normalised traces

Reference

Software citation on Zenodo:

Luke Sorensen, Ayame Saito, Sabrina Poon, Myat Noe Han, Adam Humenick, Keith Mutunduwe, Christie Glennan, Narges Mahdavian, Simon JH Brookes, Rachel M McQuade, Jaime PP Foong, Sebastian K. King, Estibaliz Gómez-de-Mariscal, Robert Haase, Simona Carbone, Nicholas A. Veldhuis, Daniel P. Poole, & Pradeep Rajasekhar (2022). Gut Analysis Toolbox (1.0.0). Zenodo. doi: 10.5281/zenodo.6095590

To download the training data, notebooks and associated models please go to the following Zenodo link:

DOI